The functional difference between long helix (index) and traditional spring wound (brake) housing is how they flex. In technical jargon it's related to the location of the neutral axis.

In a brake housing the coils of the spring lay against each other and cannot be compressed, so when the cable is flexed the inside of the curve remains a constant length and the outside of the curve opens up becoming longer. (imagine a Slinky flexed into an arc) This means that the distance down the center of the housing gets longer also, which could be problematic for index which requires a constant length housing.

Index housing is wound the long way, and flexes like a solid tube, compressing on the inside of the curve and stretching on the outside (and usually ovalizing somewhat) so that the neutral axis (place of no length change) is right down the center, assuring a constant length for the inner wire to run through.

In practice I'm not sure that it really makes a world of difference, because there isn't that much change in the curvature of the housing once the bike is set up, though with suspension or other sources of housing flex while riding the type of housing becomes more important.

In your shoes, I'd email the Shimano or the source and ask if it was a mistake. If not, I'd go ahead and use the housing and see how it performs. No sense, spending dough to replace it unless you have to.